humarray (version 1.0.0)

get.immunobase.snps: Download GWAS hits from t1dbase.org

Description

Retrieve human disease top GWAS hits from t1dbase in build hg19 coords (37). 28 Diseases currently available

Usage

get.immunobase.snps(disease = "T1D", snps.only = TRUE, show.codes = FALSE)

Arguments

disease

integer (1-28), or character (abbreviation), or full name of one of the listed diseases. A full list of options can be obtained by setting show.codes=TRUE.

snps.only

logical, default is just to return a list of rs-ids. Setting FALSE gives a table

show.codes

logical, if set to TRUE, instead of looking up t1dbase, will simply return a table of available diseases with their index numbers and abbreviations.

Value

A character vector of SNP rs-ids

References

PMID: 20937630

Examples

get.immunobase.snps(disease="CEL") # get SNP ids for celiac disease
get.immunobase.snps(disease="AS") # get SNP ids for Ankylosing Spondylitis in build-37/hg19
get.immunobase.snps(show.codes=TRUE) # show codes/diseases available to download
get.immunobase.snps(disease=27) # get SNP ids for Alopecia Areata
get.immunobase.snps("Vitiligo")